Mercurial > repos > gga > apollo_export
diff list_organisms.py @ 0:b4a85d0c85b8 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author | gga |
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date | Mon, 11 Sep 2017 05:47:07 -0400 |
parents | |
children | 950fb2bf116d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/list_organisms.py Mon Sep 11 05:47:07 2017 -0400 @@ -0,0 +1,22 @@ +#!/usr/bin/env python +from __future__ import print_function + +import argparse +import json + +from webapollo import AssertUser, WAAuth, WebApolloInstance, accessible_organisms + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='List all organisms available in an Apollo instance') + WAAuth(parser) + parser.add_argument('email', help='User Email') + args = parser.parse_args() + + wa = WebApolloInstance(args.apollo, args.username, args.password) + + gx_user = AssertUser(wa.users.loadUsers(email=args.email)) + all_orgs = wa.organisms.findAllOrganisms() + + orgs = accessible_organisms(gx_user, all_orgs) + + print(json.dumps(orgs, indent=2))